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Unverified Commit 6e073b48 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2317 from jing-huang/master 

Support CHARMM psf that contains colinear type of lonepair.
parents 325fead1 75bedabe
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Showing with 3528 additions and 777 deletions
wrappers/python/CMakeLists.txt
View file @ 6e073b48
......@@ -59,6 +59,7 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.cif"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rtf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.crd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.gro"
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 6e073b48
......@@ -366,25 +366,30 @@ class CharmmPsfFile(object):
holder = psfsections['NUMLP NUMLPH'][1]
lonepair_list = TrackedList()
if numlp != 0 or numlph != 0:
lp_hostnum_list=[]
lp_distance_list=[]
lp_angle_list=[]
lp_dihe_list=[]
for i in range(numlp):
lpline = holder[i].split()
if len(lpline)!=6 or lpline[0] != '3' or lpline[2] != 'F' or int(lpline[1]) != 4*i+1 :
if len(lpline)!=6 or lpline[2] != 'F' :
raise CharmmPSFError('Lonepair format error')
else:
lp_hostnum_list.append(int(lpline[0]))
lp_distance_list.append(float(lpline[3]))
lp_angle_list.append(float(lpline[4]))
lp_dihe_list.append(float(lpline[5]))
lp_atom_counter=0
for i in range(numlp):
lpline = holder[int(i/2)+numlp].split()
icolumn = (i%2) * 4
id1=int(lpline[icolumn]) -1
id2=int(lpline[icolumn+1])-1
id3=int(lpline[icolumn+2])-1
id4=int(lpline[icolumn+3])-1
lonepair_list.append([id1, id2, id3, id4, lp_distance_list[i], lp_angle_list[i], lp_dihe_list[i]])
idall=[]
for j in range(lp_hostnum_list[i]+1):
iline = int((lp_atom_counter+j)/8)+numlp
icolumn = (lp_atom_counter+j)%8
idall.append(int(holder[iline].split()[icolumn])-1)
if len(idall)==3:
idall.append(-1) # use id4=-1 to mark colinear
lonepair_list.append([idall[0], idall[1], idall[2], idall[3], lp_distance_list[i], lp_angle_list[i], lp_dihe_list[i]])
lp_atom_counter += lp_hostnum_list[i]+1
# In Drude psf, here comes anisotropic section
if IsDrudePSF:
numaniso = psfsections['NUMANISO'][0]
......@@ -709,6 +714,7 @@ class CharmmPsfFile(object):
if atom.type is not None:
# This is the most reliable way of determining the element
atomic_num = atom.type.atomic_number
if atomic_num != 0:
elem = element.Element.getByAtomicNumber(atomic_num)
else:
# Figure it out from the mass
......@@ -906,16 +912,18 @@ class CharmmPsfFile(object):
bond.bond_type.req*length_conv)
# Add virtual sites
if hasattr(self, 'lonepair_list'):
if verbose: print('Adding lonepairs...')
for lpsite in self.lonepair_list:
index=lpsite[0]
atom1=lpsite[1]
atom2=lpsite[2]
atom3=lpsite[3]
if lpsite[4] > 0 : #relative
if atom3 > 0:
if lpsite[4] > 0 : # relative lonepair type
r = lpsite[4] /10.0 # in nanometer
xweights = [-1.0, 0.0, 1.0]
elif lpsite[4] < 0: # bisector
elif lpsite[4] < 0: # bisector lonepair type
r = lpsite[4] / (-10.0)
xweights = [-1.0, 0.5, 0.5]
theta = lpsite[5] * pi / 180.0
......@@ -923,6 +931,15 @@ class CharmmPsfFile(object):
p = [r*cos(theta), r*sin(theta)*cos(phi), r*sin(theta)*sin(phi)]
p = [x if abs(x) > 1e-10 else 0 for x in p] # Avoid tiny numbers caused by roundoff error
system.setVirtualSite(index, mm.LocalCoordinatesSite(atom1, atom3, atom2, mm.Vec3(1.0, 0.0, 0.0), mm.Vec3(xweights[0],xweights[1],xweights[2]), mm.Vec3(0.0, -1.0, 1.0), mm.Vec3(p[0],p[1],p[2])))
else: # colinear lonepair type
# find a real atom to be the third one for LocalCoordinatesSite
for bond in self.bond_list:
if (bond.atom1.idx == atom2 and bond.atom2.idx != atom1):
a3=bond.atom2.idx
elif (bond.atom2.idx == atom2 and bond.atom1.idx != atom1):
a3=bond.atom1.idx
r = lpsite[4] / 10.0 # in nanometer
system.setVirtualSite(index, mm.LocalCoordinatesSite(atom1, atom2, a3, mm.Vec3(1.0, 0.0, 0.0), mm.Vec3(1.0,-1.0, 0.0), mm.Vec3(0.0, -1.0, 1.0), mm.Vec3(r,0.0,0.0)))
# Add Bond forces
if verbose: print('Adding bonds...')
force = mm.HarmonicBondForce()
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 6e073b48
......@@ -116,8 +116,8 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_drude(self):
"""Tests CHARMM systems with Drude force field"""
def test_Drude(self):
"""Test CHARMM systems with Drude force field"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
......@@ -136,6 +136,29 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, -1831.54, delta=0.5)
def test_Lonepair(self):
"""Test the lonepair facilities, in particular the colinear type of lonepairs"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/chlb_cgenff.psf')
crd = CharmmCrdFile('systems/chlb_cgenff.crd')
params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
'systems/par_all36_cgenff.prm')
plat = Platform.getPlatformByName('Reference')
system = psf.createSystem(params)
con = Context(system, VerletIntegrator(2*femtoseconds), plat)
con.setPositions(crd.positions)
init_coor = con.getState(getPositions=True).getPositions()
# move the position of the lonepair and recompute its coordinates
plp=12
crd.positions[plp] = Vec3(0.5, 1.0, 1.5) * angstrom
con.setPositions(crd.positions)
con.computeVirtualSites()
new_coor = con.getState(getPositions=True).getPositions()
self.assertAlmostEqual(init_coor[plp][0]/nanometers, new_coor[plp][0]/nanometers)
self.assertAlmostEqual(init_coor[plp][1]/nanometers, new_coor[plp][1]/nanometers)
self.assertAlmostEqual(init_coor[plp][2]/nanometers, new_coor[plp][2]/nanometers)
def test_InsCode(self):
""" Test the parsing of PSF files that contain insertion codes in their residue numbers """
psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
......
wrappers/python/tests/systems/chlb_cgenff.crd 0 → 100644
View file @ 6e073b48
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
*
13 EXT
1 1 CHLB C1 1.3878616207 -0.0212925645 0.0000000000 CHLB 1 -0.1000000000
2 1 CHLB H1 1.9158187876 -0.9626017904 0.0000000000 CHLB 1 0.1500000000
3 1 CHLB C2 2.0909297432 1.1920897951 -0.0000000000 CHLB 1 -0.1150000000
4 1 CHLB H2 3.1713458379 1.1910776735 -0.0000000000 CHLB 1 0.1150000000
5 1 CHLB C3 1.3891041046 2.4061558141 -0.0000000000 CHLB 1 -0.1150000000
6 1 CHLB H3 1.9293927824 3.3420080347 -0.0000000000 CHLB 1 0.1150000000
7 1 CHLB C4 -0.0132207406 2.4068634907 -0.0000000000 CHLB 1 -0.1150000000
8 1 CHLB H4 -0.5543440865 3.3420028049 -0.0000000000 CHLB 1 0.1150000000
9 1 CHLB C5 -0.7124562630 1.1912684987 0.0000000000 CHLB 1 -0.1000000000
10 1 CHLB H5 -1.7916319741 1.1777934579 0.0000000000 CHLB 1 0.1500000000
11 1 CHLB C6 -0.0118030037 -0.0204026447 0.0000000000 CHLB 1 0.0600000000
12 1 CHLB CL -0.8809968380 -1.5259625634 0.0000000000 CHLB 1 -0.2100000000
13 1 CHLB LP -1.7009674118 -2.9462612145 0.0000000000 CHLB 1 0.0500000000
wrappers/python/tests/systems/chlb_cgenff.psf 0 → 100644
View file @ 6e073b48
PSF EXT CMAP CHEQ XPLOR
3 !NTITLE
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
13 !NATOM
1 CHLB 1 CHLB C1 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
2 CHLB 1 CHLB H1 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
3 CHLB 1 CHLB C2 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
4 CHLB 1 CHLB H2 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
5 CHLB 1 CHLB C3 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
6 CHLB 1 CHLB H3 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
7 CHLB 1 CHLB C4 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
8 CHLB 1 CHLB H4 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
9 CHLB 1 CHLB C5 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
10 CHLB 1 CHLB H5 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
11 CHLB 1 CHLB C6 CG2R61 0.600000E-01 12.0110 0 0.00000 -0.301140E-02
12 CHLB 1 CHLB CL CLGR1 -0.210000 35.4530 0 0.00000 -0.301140E-02
13 CHLB 1 CHLB LP LPH 0.500000E-01 0.00000 -1 0.00000 -0.301140E-02
13 !NBOND: bonds
1 2 1 3 3 4 3 5
5 6 5 7 7 8 7 9
9 10 9 11 11 1 11 12
12 13
18 !NTHETA: angles
2 1 3 2 1 11 3 1 11
1 3 4 1 3 5 4 3 5
3 5 6 3 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 10 9 11
1 11 9 1 11 12 9 11 12
24 !NPHI: dihedrals
1 3 5 6 1 3 5 7
1 11 9 7 1 11 9 10
2 1 3 4 2 1 3 5
2 1 11 9 2 1 11 12
3 1 11 9 3 1 11 12
3 5 7 8 3 5 7 9
4 3 1 11 4 3 5 6
4 3 5 7 5 3 1 11
5 7 9 10 5 7 9 11
6 5 7 8 6 5 7 9
7 9 11 12 8 7 9 10
8 7 9 11 10 9 11 12
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0
1 0 !NGRP NST2
0 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1
1 3 !NUMLP NUMLPH
2 1 F 1.64000 0.00000 0.00000
13 12 11
0 !NCRTERM: cross-terms
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